Monday, June 19, 2006

I'm off to the UK shortly, for a workshop on "Uncertainty, Probability, Models and Climate Change". It is such a highly top secret event that there is nothing about it on the web - in fact, there doesn't seem to be a programme yet at all - but that's ok cos it doesn't start until next week :-)

I understand that workshops such as this one represent the new NERC funding model - they won't actually pay anyone to do any research any more, but they will pay for us to talk to each other about what we would do if we had any money :-) I'm not complaining because I get a ticket home and I'm having a few extra days of holiday while I am there.

I'm giving two talks, which I've put here and here. I'm hoping that the first in particular will provoke a bit of discussion - the list of attendees includes some of those who have published extremely alarming "pdfs" in prominent journals, so it will be interesting to hear their defence.

So I spoke too soon. It seems that Japan has rounded enough of its mercenaries to actually win a vote for once. Does it matter? Some conservationists seem to be getting very upset, but I find John Quiggin's comments to be very reasonable. There are no compelling moral or ethical arguments (except perhaps for the hardcore meat-is-murder types - but aren't 2,000 chickens worth more than 1 whale to them anyway?) so making decisions on the basis of reasonably democratic voting is probably the best we can do.

Sunday, June 18, 2006

Japan's hopes to buy up the IWC seem to have run aground for the time being at least. I have to say I have little sympathy for either side in this debate. On the one hand, we have the sentimentalism and symbolism of the anti-whalers, and on the other, the pork-barrel politics of a few local interests and nationalist flag-wavers.

Saturday, June 17, 2006

This sort of stuff scares me about living in Japan. The police have completely draconian powers, and routinely hold suspects for up to 3 weeks - completely incommunicado, their families often don't even get told what has happened - on any completely trivial charges while they try to coerce the victim into signing a confession. Conviction rates are about 99%, by the way.

In this case, the offence was that a bar owner didn't have the correct set of licenses for late-night dancing. So this apparently warranted 60 policemen storming the bar on a Saturday night, harassing all the foreigners who happened to be there, and imprisoning the owner for 10 days. I understand the standard treatment in Japan for suspects is several days of sleep deprivation, and interrogation with threats. And this guy got 10 days of it for a technical licence violation. It doesn't seem overly cynical to suspect that his real crime was the posession of a Peruvian nationality.

I suppose the majority of Japanese shrug their shoulders and assume it will not happen to them (and of course they are right). Perhaps it's not so different to how things are heading in the rest of the world. Indeed, you could perhaps argue that it is still better here - at least they didn't shoothim, beat him up, or kidnap him and send him abroad to be tortured. But still, it leaves me feeling somewhat uneasy.

And this time the Comment on Hegerl et al is definitely in the bin. No surprise there, and I did appreciate getting a more reasonably-worded explanation along with the rejection this time. It still seems odd that they say they might be prepared to consider it if and only if we remove any suggestion that it has implications beyond that one specific paper, but they have obviously made their final decision on that point. I'm not going to pursue that approach for the time being - we are off to the UK next week for a workshop on uncertainty in climate change, and I intend to talk about these issues so hopefully we'll get some useful feedback from a wider audience.

Meanwhile, the Comment on Frame et al has been revised and resubmitted, and can be found here. In light of the reply and reviews, we've tried to point out more explicitly where we have significant points of disagreement. We'll probably see how that fares before planning our next move. In the time it's taken, we could probably have got a stand-alone paper done and dusted, but I still think there are good reasons for pursuing it as a Comment and Reply.

Friday, June 16, 2006

This looks like a really nice piece of research. Kevin Vranes, take note :-)

No, really, that last comment was meant as a joke. But the findings of the paper certainly ring true to me - there's nothing that provokes a good flame war more than a few put-downs, subtle or otherwise. The internet is full of people doing the equivalent of bidding $3.71 for a (known) $1 prize.

Since Kevin raised the issue, I thought I would present some of the arguments against the campaign for compulsory helmet use for cyclists. Unfortunately, few people come to the debate with a sufficiently open mind as to allow the facts to influence their beliefs, but here goes anyway:

Cycling is already safe and not in any way deserving of special safety equipment

The health benefits of cycling massively outweigh the risks

Helmets are pretty useless anyway, and can be expected to make some types of brain injury worse

Risk compensation means that those who believe helmets to be useful will not be safer

There are many higher priorities for safe(r) roads

Heat stress is a real issue (sometimes)

There is no evidence from population studies that helmet legislation (or increased wearing) makes cycling safer

There are many detailed explanations of the above points to be found on the internet, eg here and here. It's not necessary to accept all the above points in order to conclude that helmet legislation (and perhaps even promotion of their wearing) is at best a distraction from the real issues, and more likely actually damaging in terms of public health alone, let alone the sort of values that we claim to hold dear (eg freedom from unnecessary interference by pettifogging bureaucrats and shroud-waving nannying do-gooders).

I used to routinely wear a helmet when cycling, but gradually came to realise, as I investigated the subject, that there wasn't really any justification for it. In Japan, the summer is hot enough that it was really unpleasant and definitely distracting. The final straw was on discovering a trivial error in a published study, the correction of which demonstrated that their data actually showed helmets to have (at best) a minor influence on safety rather than being the dominant factor they had claimed them to be. The authors' response was basically to say that they still believed their main conclusions even though the data didn't support it! If that is the best they can come up with, I'm distinctly unimpressed. Most of the other oft-cited studies have well-known flaws - in the most infamous example of which, the authors produced a revised analysis (showing a lower benefit from helmet wearing than their original work) but the incorrect (but more impressive) figures are still routinely cited by "safety campaigners".

There are, of course, several differences between powered two-wheelers and bicycles, which may tip the balance more in favour of helmets for the former (I don't claim to know much about the m/c case). But I'm disappointed that Kevin's promised "risk analysis" consists of nothing more than "it's common sense innit". The evidence clearly indicates otherwise, for me anyway. And how many of the "it's common sense innit" crowd wear walking helmets, or even buy them for their children?

Tuesday, June 13, 2006

Well whoopdedoo. I suppose there is no real reason to actually complain, but for people with jobs, getting a visa extension is generally not that big a deal.

Tenure, employment rights, permanent residency and citizenship are where the real issues are. Will the Govt actually address these substantively? I wouldn't advise anyone (gitwizards aside) to hold their breath.

As one of the comments on the news article mentions, the "gaijin tax" otherwise known as pension system is something they could usefully look at too. We have to pay in to the compulsory system, but on leaving the country, the refund is limited to about 3 years' worth of contributions. This makes it basically a state-sponsored theft from the small number of us who have been here for longer than that time. (We have no chance of actually getting a pension out of the system, which would require us to contribute for 25 straight years.) If 5 year visas become standard, they can hardly not give a 5 year refund - or can they?

Saturday, June 10, 2006

The Japanese long hours/lack of sleep culture is hardly a secret, but this article (which I've not seem publicised in Japan) suggests it's getting worse not better. However, I'm a bit suspicious of where these numbers come from. People can only achieve a certain work rate and the fact that they also spend a few hours sleeping doesn't necessarily detract from that. The Japanese also take few enough days off work that a few extra to sleep in is hardly a crime. Not that I think it's a good thing to spend long days commuting hours to work and back, only to snore loudly at the desk all day long as one of my cubicle-neighbours regularly does.

I've heard that schoolchildren sometimes fall asleep in class too, and instead of targetting them with a well-aimed chalk (or something larger) as would happen in the UK, the teachers just leave them to it. The children also have silly commutes and absurd amounts of homework. Good preparation for adult life, it seems!

This was on the front page of the JT today (at least the on-line version). Don't ask me what it means, or if it is important, but our colleagues down the road (or train line) in Yokosuka seem to think they have found something interesting. Presumably there is a forthcoming paper with more details, but the news article doesn't mention it. Perhaps it's the wrong pole for Stoat to be interested in it, but it's all ice, innit?

Nature is trialling an open peer review system (hat tip John Fleck for the pointer). There is an outline of the scheme on that page, and a series of essays about the peer review system. It's planned to run alongside their conventional anonymous peer review for 3 months, on a purely voluntary basis (ie authors can volunteer for their manuscripts to be posted and commented on publically while undergoing the standard review).

There doesn't seem to be a lot happening there yet, but there are RSS feeds for papers and comments. I'll keep an eye out for anything climate-related. The associated essays are also worth a read.

Jules is currently helping to edit a special issue of the open review EGU journal "Climate of the Past", but it's too early to see how that is going (there are no papers actually typeset and posted yet, although several have been submitted). It will be interesting to see how these ideas work out. In both cases, there is a conventional peer review (with anonymity if the reviewer chooses) with the manuscript simultaneously available for public comment.

There are a handful of papers already posted in the Nature system which seem to already be published, including this one relating climate change to a decline in some bird populations. Perhaps they were just meant to kick-start or test the system. I didn't notice any publicity about that particular paper when it was published last month - FWIW, it seems more solid than that frog thing that got so much atttention. But of course a population decline isn't as exciting as a mass extinction. Incidentally, some supposedly extinct frogs were rediscovered recently. I don't know if these are the same ones that were exterminated by global warming or not - they certainly sound related though. They are still under severe threat of course.

Tuesday, June 06, 2006

Jules is sitting in a sushi bar by herself, having lunch. In walks another gaijin (Bob) who takes the spare seat opposite. They are seated too close to play the "I'm the only gaijin in the village" game so strike up a conversation instead.

Bob: So what do you do here then?Jules: Oh, I'm a climate researcher.Bob: Funny you should say that, I've got a friend who is interested in climate. He's got this wacky idea where he goes around challenging sceptics to bet on whether the world is going to warm up.Jules: Really? But--Bob (interrupting): Yeah, he was trying to arrange something with that guy at MIT whose name begins with a W.Jules: You mean Richard Lindzen?Bob: Yup, that's the one.Jules: Wow that's bizarre. But--Bob (interrupting): Do you know about the guy who invented this thing?Jules: Well, yeah, actually--Bob: I hear all kinds of things.Jules: Yeah?Bob: Supposedly, he was born in a mental institution. And he sleeps only one hour at night. He's a great man.Jules: Oh,....--Bob: Do you know about Brian Schmidt?Jules stares at him.

Scene fades.

------Ok, I embellished the script a bit (with apologies to Chuck Palahniuk, in particular the scene which starts at these words). But in case you all think I've gone completely off my trolley, I assure you that the basic event really did place pretty much as described!

Sunday, June 04, 2006

No, this isn't going to be a boring whinge by me about the bad reviews I're received and how life isn't fair (in fact, I've had very few reviews that I have any major complaints about). The title of this post is actually the title of an interesting but flawed paper by Neff and Olden which I recently had my attention drawn to. (The full text can be found here). The authors investigate the influence of randomness in reviewer decisions, based on a very simple (but IMO fairly reasonable) model. They define the "suitability" of a paper for a journal to be the proportion of researchers who would agree that the paper should be published in that particular journal. This has the nice property that it directly accounts for a journal's perceived quality, and furthermore can be directly applied to the reviewers too (with the slight modification of the judgement to "should be published after necessary revision"). They further define the "correct" threshold for publication to be an 80% level (ie, 80% of readers/reviewers agree it should be published), and investigate the effect of changes to the review procedure (eg using more or fewer referees, possibly with an editorial pre-screening) in terms of the quality of the resulting decisions. So far so good.

It's certainly an interesting topic, and they argue that some real journal data lends support to their model. That seems perhaps a bit tenuous (it's hard to rule much in or out IMO), but still reasonably plausible to me. Where they really fluff their lines is in the calculations they present from their model. They claim to calculate the "probability of wrongful rejection" and "probability of wrongful acceptance" and present figures for these in Table 1, Fig 2 and the text. Of particular interest, they claim that the former value (wrongful rejection) remains extremely low, only increasing from 6% to 7% and then 8% when the review process is tightened considerably by moving from 2 reviewers first to 3 and then 4 respectively (each reviewer is assumed to be armed with a veto, rather than a majority vote being used). The probability of wrongful publication, on the other hand, drops from a rather worring 51% to a clearly better (but still perhaps rather high) 33% at the same time. Adding a layer of editorial review (effectively another referee, although with some differences) improves things still further. On the basis of this, they argue strongly that stiffening up the system would improve the quality of journals considerably.

It seemed immediately obvious to me that their numbers didn't pass the sniff test, so I investigated a little more carefully. What they have actually calculated is not the probability that a good manuscript is rejected (or vice versa), but instead the proportion of rejected (accepted) papers which should have been accepted (rejected). In order to do this, it is necessary to estimate (or assume) what proportion of initially submitted manuscripts are poor. The authors set this at a whopping 80%, which means that when they look at the heap of rejected manuscripts, the proportion of these which should have been published, could not possibly exceed 20% unless they reviewers actively prefer poor papers over good! So the probabilities that they present as "wrongful rejection", of around 6-10%, seem low but do not actually address the question that many researchers will want to know the answer to (and will surely expect "wrongful rejection" to refer to), which is: if I, or anyone else, write a manuscript which qualifies as "good" according to the defined criterion, what is the probability that it gets rejected?

This latter calculation is pretty trivial, and does not depend on any assumptions about how many good and bad manuscripts there are in total. Even under the weakest review system they consider, where acceptance depends on a mere 2 reviewers agreeing with publication, the real probability of a paper of 90% quality (clearly well above the defined quality threshold for publication) being rejected is actually as high as 19%, way above the 6% figure they present. With 4 reviewers, the probability of rejection for the same paper increases to a whopping 34%, and a more borderline paper of 84% quality is actually more likely to be rejected than not. Would scientists be willing to accept a system where high quality research had such a high probability of rejection? I doubt it, but I guess that is arguable, depending on how one views the relative importance of the two problems of wrongful acceptance versus wrongful rejection. More importantly, the case for more stringent review - if there is one - needs to be made on the basis of a valid representation of its likely effects rather than their rather misleading calculations.

I can't resist the small snark that perhaps the publication of this paper proves the authors' main point after all: too many poor papers get through the reviewing process as it stands :-) Perhaps that is a bit harsh - the authors are looking at the problem from the point of view of the quality of the resulting journal and the number of poor papers it is likely to contain. Of course, due to their initial assumption that the vast majority of submitted manuscripts are poor (which I suspect is substantially exaggerated), the number that make it through is quite high, and increasing the stringency of the review will help to cut down this proportion. But this comes at quite a cost (in terms of rejecting good research) which is not spelt out at all clearly in the paper.

I shouldn't laugh, but this story reminds me rather of our house. Not that we are particularly horders, just messy. Most people fear burglars breaking in and trashing their house when they are off on holiday. We reckon they would probably leave it tidier than they found it!

Along similar lines, a few years ago an ex-pat told us a story about how all their ship-load of stuff was ruined in transit by oil. Of course it must be sad to lose quite a lot of it, but (as they said) also in some ways a relief to have a solid excuse for good clear-out without having to make difficult decisions about everything. As usual, Tyler Durden hits the nail on the head (actually, we don't hate our jobs, but it's close enough).

Sometimes headlines need no further comment, but the consequences of an unmuffled Royal Sneeze at a public event are too horrible to contemplate. I am trying to control myself in the light of these shocking stories. Wouldn't do to have an accident...especially now, with this reported shortage of tissue paper :-)

The Japanese obsession with tissues is a funny thing. They are ubiquitously used as marketing devices, handed out in small packets with advertisements attached to them to passing pedestrians, and I've also seen their price used as some barometer of the cost of living in various places. IIRC, Thatcher once famously had no idea about the price of a pint of milk. I wonder if Koizumi knows what a box of tissues costs? Will the tissue issue be mentioned in Parliament?

The news on Japan's population problem doesn't get any better: Fertility rate drops to record low 1.25 in 2005. That is way below the forecasts of even a couple of years ago (in 2002 they forecast 1.31 for this year), and the actual population decline has also happened much faster than was predicted. Something has gone badly wrong with the way official forecasts have been generated - I would guess this is due to the natural instinct of politicians to pretend that long-term issues are less of a problem than they are in reality, in order to put off the problem to future Governments. Even under the optimistic official forecasts, Japan's population would be expected to halve by 2100.

Thursday, June 01, 2006

Well, following a polite enquiry to GRL, the Editor has agreed to consider a revised Comment. This seems very reasonable - as I said before, the original decision didn't actually seem to be justified by the reviews. Of course, we still have the fun of trying to satisfy 3 rather diverse reviewers within the 2 page (and 2 week) limit while trying to keep some of our own opinion in there too :-) So the final outcome is far from a foregone conclusion. Dave is engaged in some interesting email discussions with us which should make the final result more useful.

In Other News, today I also received an email from Nature saying that they are considering my "appeal" on the Hegerl et al thing. This came as somewhat of a surprise - I had sent them a rather intemperate and sarcastic email immediately following our rejection several weeks ago, and not heard anything (nor really expected to) since. Perhaps they were just clearing out the spam trap and found I'd been filtered for using naughty words (no, I didn't really). Of course I'm sure they won't take the comment, but who knows, they might give me another amusing excuse when they reconfirm the rejection :-)